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29 Aug 2014 - New ENCODE portal launched at www.encodeproject.org

The website for up-to-date information about the ENCODE project is no longer hosted here at www.genome.ucsc.edu/ENCODE. These UCSC ENCODE pages now archive information and tools from the ENCODE production and pilot phases (2003 to 2012) including live links to visualize and download data. Please navigate to the new ENCODE portal for recent data releases. Along with the ability to use faceted searching to explore all ENCODE data, the ENCODE portal provides visualization in the UCSC Genome Browser via a "Visualize Data" link on assay pages when processed data files are available.

The ENCODE Data Coordination Center is pleased to announce the first public release of data from the third phase of ENCODE. This phase represents a continuation of ENCODE and Mouse ENCODE through an additional four years of high-throughput whole-genome data production, with additional resources and emphasis on uniform data processing, analysis and functional validation. The participants and projects in this phase of ENCODE are listed here.

This data release includes the following datasets:

• Human: 257 ChIP-seq, 164 RNA-seq (includes 25 with shRNA knockdown), 22 RAMPAGE, 7 ChIA-PET, 20 RNA Bind-n-Seq
• Mouse: 260 ChIP-seq, 2 RNA-seq, 28 Shotgun Bisulfite-seq (WGBS)

• RAMPAGE: Identifies transcriptional start sites with quantification (PMID: 24510412, PMID: 22936248)
• Shotgun Bisulfite-seq (WGBS): Analyzes DNA methylation at high resolution (PMID: 19829295)
• RNA Bind-n-Seq: Identifies binding sequences and measures affinity of protein binding to RNA, using a cell-free system (PMID: 24837674)

Going forward, the DCC website and ENCODE portal will merge to provide a single site with comprehensive information about the ENCODE project and extensive user tools for locating data of interest from all phases of ENCODE production. The ENCODE tools, tracks, and downloads developed during the first production phase will remain available at the UCSC Genome Browser site, http://genome.ucsc.edu/ENCODE. For newer data, the 'Visualize Data' button under the Files section of the new site's Experiment pages launches a Genome Browser view for processed data suitable for visualization.

The new data is released under a rapid release policy by which primary data (e.g. fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for this data. The new data release policy is available here.

The latest Transcription Factor ChIP-seq track has been enhanced with the display of Factorbook motifs. Within a cluster, a green highlight indicates the highest scoring site of a Factorbook-identified canonical motif for the corresponding factor. Along with the ability to suppress motif highlights and cell abbreviations, the track configuration page now also enables the filtering of factors.

The newly added Genome Segmentations from ENCODE tracks display multivariate genome-segmentation performed on six human cell types (GM12878, K562, H1-hESC, HeLa-S3, HepG2, and HUVEC), integrating ChIP-seq data for eight chromatin marks, RNA Polymerase II, the CTCF transcription factor and input data. In total, twenty-five states were used to segment the genome, and these states were then grouped and colored to highlight predicted functional elements. These Genome Segmentations are the same data as found in the Analysis Working Group Hub, but now hosted natively in the Browser with enhanced filtering capability where desired segmented states can be selected using the 'Filter by Segment Type' control on the track configuration page.

12 Sept 2013 - New UDR ENCODE Download Method Available

The UCSC Genome Browser is pleased to offer a new download protocol to use when downloading large sets of files from our download servers: UDR (UDT Enabled Rsync). UDR utilizes rsync as the transport mechanism, but sends the data over the UDT protocol, which enables huge amounts of data to be downloaded efficiently over long distances.

Remember that we now have two identical download servers to better serve your needs. You can use either one:

http://hgdownload.cse.ucsc.edu

http://hgdownload-sd.sdsc.edu

The Background:

Typical TCP-based protocols like http, ftp and rsync have a problem in that the further away the download source is from you, the slower the speed becomes. Protocols like UDT/UDR allow for many UDP packets to be sent in batch, thus allowing for much higher transmit speeds over long distances. UDR will be especially useful for users who are downloading from places that are far away from California. The US East Coat and the international community will likely see much higher download speeds by using UDR rather than rsync, http or ftp.

Getting UDR & Setting it up on your System:

It should be noted that UDR is not written or managed by UCSC, it was written by the Laboratory for Advanced Computing at the University of Chicago. It has been tested to work under Linux, FreeBSD and Mac OSX, but may work under other UNIX variants. The source code can be obtained here, through GitHub:

https://github.com/LabAdvComp/UDR

If you need help building the UDR binaries or have questions about how UDR functions, please read the documentation on the GitHub page, and if necessary, contact the UDR authors via the GitHub page. We recommend reading the documentation on the UDR GitHub page to better understand how UDR works. UDR is written in C++. UDR is Open Source and is released under the Apache 2.0 License. You must first have rsync installed on your system.

For your convenience, we are offering a binary distribution of UDR for Red Hat Enterprise Linux 6.x (or variants such as CentOS 6 or Scientific Linux 6). You'll find both a 64-bit and 32-bit rpm here:

http://hgdownload.cse.ucsc.edu/admin/udr

Using UDR to Download ENCODE Data from the UCSC Genome Browser Download Server(s):

Once you have a working UDR binary, either by building from source or by installing the rpm (if you are using RHEL 6.x or other variant), you can download files from either of our our download servers in a very similar fashion to rsync. For example, using rsync, you may want to download all of the ENCODE information for the mm9 database using the following command:

$ rsync -avP rsync://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/ /my/local/mm9/

Using UDR is very similar. The UDR syntax for downloading the same data would be:

$udr rsync -avP hgdownload.cse.ucsc.edu::goldenPath/mm9/encodeDCC/ /my/local/mm9/

If you installed the rpm, use the 'man udr' command for more information via the man page; if you installed from source please refer to the UDR GitHub page for more details on the capabilities of UDR and how to use it.

Firewall Considerations:

UDR establishes connections on TCP/9000, then transmits the data stream over UDP/9000-9100. Your institution may need to modify its firewall rules to allow inbound and outbound ports TCP/9000 and UDP/9000-9100 from either of the two download machines.

If you decide to install and use UDR, we hope that you experience greatly increased download speeds. If you have difficulties installing UDR on your system, please contact the Laboratory for Advanced Computing through their gitHub page: https://github.com/LabAdvComp/UDR.

25 July 2013 - BLUEPRINT Epigenome Data Hub and Quick Reference PDF Now Available

We are pleased to announce the addition of the BLUEPRINT Epigenomics Data Hub on the UCSC Genome Browser through our Public Hubs function. All data were produced and processed by the European BLUEPRINT Epigenome project, aimed to generate 100 reference epigenomes from distinct types of haematopoietic cells and their malignant leukaemic counterparts. Please send any data related questions to [email protected]. The BLUEPRINT Hub currently contains 8 DNase-seq, 48 DNA methylation, 170 Histone modification, and 24 RNA-seq tracks, focused on displaying variation in human monocyte and neutrophil cells from 7 adult blood and 4 cord blood samples. Future releases of data for additional samples are planned at a regular basis.

Also the ENCODE Quick Reference Card is now available in PDF courtesy of OpenHelix on the ENCODE Education and Outreach page.

The ENCODE portal was updated to include informative new and expanded pages. A new link to the NHGRI ENCODE Tutorials was added to the ENCODE Education and Outreach page. A new External Software Tools page was added to expand the existing ENCODE Software Tools resources page. The Publications page was expanded to include a new 2013 Consortium-funded section and updated with several new references as well as the non-ENCODE Publications page. Lastly other pages were updated with new information including the ENCODE Analysis Software page, and Quality Metrics page.

UCSC has released a new browser track containing 690 datasets of transcription factor ChIP-seq peaks based on data from all five ENCODE TFBS ChIP-seq production groups from the project inception in 2007 through the ENCODE March 2012 data freeze. The track covers 161 unique regulatory factors (generic and sequence-specific factors), spanning 91 human cell types, some under various treatment conditions.

Browser track: Transcription Factor ChIP-seq Uniform Uniform Peaks from ENCODE/Analysis
File downloads: Directory File selection tool

This track represents peak calls (regions of enrichment) generated by the ENCODE Analysis Working Group (AWG) using the uniform processing pipeline developed for the ENCODE Integrative Analysis effort and published in a set of coordinated papers in September 2012. Peak calls from that effort (based on datasets from the January 2011 ENCODE data freeze) are available at the ENCODE Analysis Data Hub. The new Uniform TFBS track at UCSC includes newer data, slightly modified processing methods, and improved metadata. Quality metrics are included in metadata, with detailed metrics in a quality spreadsheet linked to the track description. Browser users will see the uniform peaks first when using track search for TFBS, and this track is now the default track shown when the ENCODE TF Binding menu item is selected in the browser.

The primary and lab-processed data (along with methods descriptions, credits and references) on which this track is based are available in the following ENCODE tracks: HAIB TFBS, SYDH TFBS, UChicago TFBS, UTA TFBS, UW CTCF Binding. Many thanks to Anshul Kundaje of the ENCODE AWG for providing the uniform peaks data, description, and quality spreadsheets.

This new page provides links to ENCODE informational material and tools at the NHGRI, GEO, UCSC, and Nature, together with links to some of the most useful pages at encodeproject.org. It also includes a helpful FAQ section culled from ENCODE questions received on the ENCODE and Genome Browser mailing lists.

The ENCODE Analysis Working Group (AWG) has performed uniform processing on datasets produced by multiple data production groups in the ENCODE Consortium. The AWG uniform datasets are used in downstream analysis pipelines by members of the ENCODE Consortium and are one of the primary sources of data referenced in the 2012 ENCODE integrative analysis.

UCSC has released a new browser track and a track update based on the AWG uniform processing of ENCODE DNaseI data:

DNaseI Hypersensitivity Uniform Peaks from ENCODE/Analysis: This track displays the uniform set of open chromatin elements in 125 ENCODE cell types on a per-cell type basis.

Digital DNaseI Hypersensitivity Clusters in 125 cell types from ENCODE: This track displays clusters of Uniform DNaseI Hypersensitive sites across the cell types assayed. This is the second release of the Dnase Clusters track, which is part of the ENCODE Regulation supertrack in the Genome Browser. It contains 51 additional cell type + treatment combinations. It differs from the previous track by including data from multiple ENCODE groups that have been uniformly processed, with replicates merged. The previous track is available on the UCSC preview browser as DNase Clusters V1.

The uniform elements in these tracks are based on DNase-seq data produced by the "Open Chromatin" (Duke/UNC/UT-A) and University of Washington (UW) ENCODE groups from the project inception in 2007 through the ENCODE January 2011 data freeze. The primary and lab-processed data (along with methods descriptions, credits and references) on which these tracks are based are available in the following ENCODE tracks: ENCODE Duke DNaseI, ENCODE UW DnaseI HS.

To supplement the existing ENCODE Foundations tutorial, OpenHelix has developed a second tutorial describing newer ENCODE data and access tools. Slides for this tutorial are freely available through March 2013 from the website at: http://openhelix.com/ENCODE2. Also available free (up to 30 cards shipped free in the US) is a Quick Reference Card that provides a handy summary of access features. For more information see the OpenHelix announcement.

Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ: This track displays mass spectrometry data that have been matched to genomic sequences in GM12878, H1-hESC, H1-neuron, and K562 cell types. Peptides were mapped to an in silico translation and proteolytic digestion of the whole human genome (UCSC Hg19), and the GENCODE translation of protein-coding transcripts database. The track can be used to identify which parts of the genome are translated into proteins, to verify which transcripts discovered by other ENCODE experiments are protein-coding, to reveal new genes and/or splice variants and proteins with post-translational modifications (PTM). Of particular interest is the possibility of uncovering the translation of small open reading frames (ORFs), antisense transcripts, or protein-coding regions that have been annotated as introns previously.

Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill) (Release 2): FAIRE (Formaldelhyde-Assisted Isolation of Regulatory Elements) is a method to isolate and identify nucleosome-depleted regions of the genome. Release 2 of this track contains 12 new experiments, including 11 new cell lines.

Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB (Release 3): This release contains 110 new experiments including 3 new cell lines. There were also data corrections (see Release Notes section for details).

Long RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 3): This release contains additional files for many experiments including GENCODE V10 referenced Transcripts, Genes and Exons (previous datasets referenced GENCODE V7). Complete details are in the track Release Notes.

DNaseI Digital Genomic Footprinting from ENCODE/University of Washington: This track contains deep sequencing DNase data that can be used to identify sites where regulatory factors bind to the genome (footprints). Footprinting is a technique used to define the DNA sequences that interact with and bind DNA-binding proteins, such as transcription factors, zinc-finger proteins, hormone-receptor complexes, and other chromatin-modulating factors like CTCF. The technique depends upon the strength and tight nature of protein-DNA interactions. This track contains a total of 22 DGF experiments, covering 20 mouse cell types and tissues.

DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington (Release 2): Adds 32 new experiments including 22 new cell lines and 4 new treatments.

Histone Modifications by ChIP-seq from ENCODE/LICR (Release 3): Adds 31 new experiments for a total of 130 experiments.

Long RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 3): This release adds data for bladder, cerebellum, CNS, cortex, frontal lobe, limb, liver, placenta, and whole brain. The samples for CNS, liver, limb and whole brain vary over age (developmental stage). This release also contains replacement BAM files for the previous ones had the second read reverse complemented.

The results of the ENCODE project were published today in a coordinated set of 30 papers published in multiple journals. These publications are the result of cross-consortium integrative analysis, covering more than 4 million regulatory regions in the human genome mapped as part of ENCODE. The coordinated publication set includes one main integrative paper and five other papers in the journal Nature; 18 papers in Genome Research; and six papers in Genome Biology. The ENCODE data are so complex that the three journals have developed a pioneering way to present the information in an integrated form they term "threads." Since the same topics were addressed in different ways in different papers, the Nature ENCODE website was developed to allow readers to follow a topic through all of the papers in the ENCODE publication set. In addition to these publications, six review articles are being published in the Journal of Biological Chemistry, and other affiliated papers in Science, Cell, and other journals. The new Integrative Analysis page on this portal provides links and descriptive material for these publications and related analysis resources.

DNaseI Digital Genomic Footprinting from ENCODE/University of Washington (Release 4) Adds 10 new experiments across 8 cell lines.

Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University) (Release 3): Adds 27 new experiments including 18 new cell lines.

Histone Modifications by ChIP-seq from ENCODE/Broad Institute (Release 3): Adds 83 new experiments including 6 new cell lines and 25 new antibodies.

RNA Sub-cellular Localization by Paired-end diTag Sequencing from ENCODE/GIS (Release 2): Adds data for 4 additional cell lines (A549 lung carcinoma, SK-N-SH neuroblastoma, IMR90 lung fibroblast, and MCF-7 breast carcinoma).

Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard (Release 3): Adds 37 new experiments including 1 new cell line (SK-N-SH neuroblastoma) and 7 new antibodies.

Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) (Release 2) : Adds 34 new experiments including 17 new cell lines.

DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU

This track provides maps of DNaseI sensitivity in G1E (GATA- erythroid progenitor cells) untreated and differentiated via estradiol treatment. DNaseI has long been used to map general chromatin accessibility, and DNaseI hypersensitivity is a universal feature of active cis-regulatory sequences.

Histone Modifications by ChIP-seq from ENCODE/PSU (Release 2): This release adds one new experiment (H3K4me1 in G1E cells).

Histone Modifications by ChIP-seq from ENCODE/SYDH (Release 2): This release adds 12 new experiments, including 1 new cell line (E14 ES cells) and 5 new antibodies.

Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU (Release 2): This release adds 14 new experiments.

Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale (Release 4): This release adds 22 experiments including 12 new antibodies.

DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington (Release 6): Includes 11 new experiments across 12 new cell lines: bone marrow HS27a, bone marrow HS5, bone marrow MSC, CD4+ Naive Wb11970640, CD4+ Naive Wb78495824, Th17, Th1 Wb33676984, Th1 Wb54553204, Th2 Wb33676984, Th2 Wb54553204, Treg Wb78495824, Treg Wb83319432.

DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlpha (Release 3): Adds the MCF-7 cell line with shRNA knockdowns obtained from the Crawford Lab at Duke University.

Replication Timing by Repli-chip from ENCODE/FSU (Release 2): Adds 6 more data sets including additional replicates for H1-hESC and H7-hESC and all new data for the iPS skin fibroblast bio samples.

Affymetrix Exon Array from ENCODE/University of Washington (Release 4) (2012-07-31): Adds in H7-hESC cells that have been differentiated with different time courses.

Replication Timing by Repli-chip from ENCODE/FSU: shows genome-wide assessment of DNA replication timing using NimbleGen tiling CGH microarrays. Each experiment represents the relative enrichment of early vs. late S-phase nascent strands in a given cell line, with data represented as a loess-smoothed function of individual timing values at probes spaced at even intervals across the genome. Regions with high values indicate domains of early replication where initiation occurs earlier in S-phase or early in a higher proportion of cells.

RNA-seq from ENCODE/UW: shows RNA-seq measured genome-wide in 25 mouse tissues and cell lines. Poly-A selected mRNA was used as the source for transcriptome profiling of tissues and cell types that also had corresponding DNase I hypersensitive profiles.

Long RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 2): includes a new browser view (Splice Junctions) and 6 new analysis files per experiment (de novo exons, genes and transcripts with expression levels defined by Cufflinks and Flux Capacitor, and expression levels for Ensembl and Cufflinks models at each level).

Small RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 3) : adds 53 additional experiments, with twenty-two new cell lines represented: CD20+, CD34+_Mobilized, HAoAF, HAoEC, HCH, HFDPC, HMEpC, hMSC-AT, hMSC-UC, HOB, HPC-PL, HPIEpC, HSaVEC, HVMF, HWP, IMR90, Monocytes-CD14+, NHDF, NHEM.f_M2, NHEM_M2, SkMC, SK-N-SH. There are also two new variations in protocol (CIP-TAP and untreated) used to create different RNA populations.

UCSC Integrated Regulation: Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE: includes transcription levels for 2 additional cell lines: HeLa-S3 and HepG2.

Affymetrix Exon Array from ENCODE/University of Washington (Release 3): revokes previously released K562 zinc-finger experiments due to a data merging issue.

Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass. (Release 2): contains reanalyzed peak files and more complete raw data.

The ENCODE Consortium analysis working group has analyzed the quality of the data produced using a variety of metrics. The ENCODE portal Quality Metrics page provides spreadsheets showing quality metrics for human ENCODE datasets, along with descriptions of what the metrics are and what they appear to measure. Spreadsheets are provided for DNase-seq, FAIRE-seq, Transcription Factor ChIP-seq, Histone ChIP-seq, and ChIP Controls. This page is linked from the related Data Standards page. Many of the software tools used for quality metrics, along with their citations, can be found on the portal Software Tools page.

26 Jun 2012 - Human ENCODE data releases: GENCODE Genes V12, CSHL Long RNA-seq (Release 2), SYDH Histone (Rel 3), UW DNaseI HS (Rel 5)

Gene Annotations from ENCODE/GENCODE Version 12: This version is based on the Ensembl 67 (May 2012) and Vega 47 (April 2012) gene predictions and curation.

Long RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 2): includes 25 new cell lines: CD20+, CD34+_Mobilized, HAoAF, HAoEC, HCH, HFDPC, HMEpC, hMNC-CB, hMNC-PB, hMSC-AT, hMSC-BM, hMSC-UC, HOB, HPC-PL, HPIEpC, HSaVEC, HVMF, HWP, IMR90, Monocytes-CD14+, NHDF, NHEM.f_M2, NHEM_M2, SkMC, and SK-N-SH. The downloadable elements files (Transcripts, Genes and Exons) in this release were generated using GENCODE V10, while the older datasets were generated using GENCODE V7.

Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard (Release 3): adds 9 new experiments for the MCF-7, HCT-116 and PANC-1 cell lines.

DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington (Release 5): adds 11 experiments across 9 new cell lines.

25 Jun 2012 - Mouse ENCODE data releases: Stan/Yale RNA-seq, Stan/Yale TFBS (Release 3) :

One new track and one track update were released on the mm9 genome browser:

RNA-seq from ENCODE/Stanford: This track shows enrichment of RNA sequence tags mapped to the mouse genome generated by high throughput sequencing in CH12, MEL, and ES cells.

Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale (Release 3): adds 17 new experiments, for a total of 54 experiments, studying 26 factors in CH12, MEL and ES cells.

15 Jun 2012 - Mouse Experiment Matrix web tool

The ENCODE DCC at UCSC has released an 'Experiment Matrix' for Mouse ENCODE data on the portal. The three web pages in this application (Experiment Matrix, Experiment Summary, and ChIP-seq Experiment Matrix) provide an up-to-date view of the publicly available Mouse ENCODE data, along with an interface for selecting experiments for viewing in the browser or downloading as files for analysis. Each page has a file/track selector. Clicking an experiment item produces a search window with resulting files or tracks listed.

The pages are best viewed in Firefox, Chrome, and Safari browsers, and zoomed out as far as readability on your screen allows.

31 May 2012 - Human ENCODE data releases: GIS ChIA-PET, SYDH TFBS (Release 2), RIKEN CAGE Loc (Release 3)

Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan:

This track shows the locations of protein factor mediated chromatin interactions determined by ChIA-PET data in five different human cancer cell lines (K562 (chronic myeloid leukemia), HCT116 (colorectal cancer), HeLa-S3 (cervical cancer), MCF-7 (breast cancer), and NB4 (promyelocytic)). The protein factors displayed in the track include estrogen receptor alpha, RNA polII, and CTCF.

Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a global de novo high-throughput method for characterizing the 3-dimensional structure of chromatin in the nucleus. A chromatin interaction is defined as the association of two regions of the genome that are far apart in terms of genomic distance, but are spatially proximate to each other in the 3-dimensional cellular nucleus.

Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard (Release 2): contains 79 new experiments.

RNA Subcellular CAGE Localization from ENCODE/RIKEN (Release 3): includes viewable Transcription Start Sites determined by Hidden Markov Models. It contains the following new cell lines and tissues: CD20+, CD34+ Mobilized, HAoAF, HAoEC, HCH, HFDPC, HMEpC, hMSC-AT, hMSC-BM, hMSC-UC, HOB, HPC-PL, HPIEpC, HSaVEC, HVMF, HWP, IMR90, Monocytes-CD14+, NHDF, NHEM.f_M2, NHEM_M2, SkMC, and SK-N-SH.

25 May 2012 - Mouse ENCODE data releases: Caltech RNA-seq, PSU Histone, LICR RNA-seq (Release 2)

Two new tracks and one track update were released on the mm9 genome browser:

RNA-seq from ENCODE/Caltech: This track shows transcriptome measurements in 10T1/2 fibroblasts and C2C12 myoblasts, and these same cell types treated with differentiation media to produce fibrocytes and myocytes. RNA-seq was performed on total cellular polyA+ RNA with 100bp paired end reads aligned to the genome.

Histone Modifications by ChIP-seq from ENCODE/PSU: This track displays levels of three histone modifications - H3K4me1 (indicative of active chromatin and enhancers), H3K4me3 (enriched at active promoters), and H3K27me3 (associated with some silenced genes), in 5 blood-derived primary cells and cell lines.

RNA-seq from ENCODE/LICR (Release 2): This release adds RNA-seq data for 12 additional primary cell types, bringing the total for this track to 22.

8 May 2012 - ENCODE Experiment Matrix web tool

The ENCODE DCC at UCSC is pleased to announce the release of a new web tool for accessing ENCODE data. The new Experiment Matrix link on the ENCODE portal leads to a set of three web pages that provide an up-to-date view of the breadth of human ENCODE data available, along with an interface for selecting experiments for viewing in the browser or downloading as files for analysis. (Note: the related Experiment List (previously 'Data Summary') spreadsheets have been updated to reflect newer status).

The main Experiment Matrix page shows the number of experiments for each cell type/assay pairing. The related ChIP-seq Experiment Matrix provides a view of the transcription factor and histone modification datasets, showing experiments by cell type and antibody target. The Experiment Summary lists the number of experiments by assay type alone and includes annotations that are cell-type independent (annotations on the reference genome). Each page has a file/track selector. Clicking an experiment item produces a search window with resulting files or tracks listed.

These pages are best viewed in FireFox, Chrome, and Safari browsers, and zoomed out as far as readability on your screen allows.

Special thanks to Katrina Learned and Steve Heitner for careful QA review and testing, to the Genome Browser build & release group for shepherding the new program to the public site, and to the DCC wranglers for the high quality metadata curation that supports this new access tool.

20 Apr 2012 - Human ENCODE data releases: UMass 5C, ENCODE Pilot Regions, FSU Repli-chip and 11 track updates

Three new tracks and 11 track updates were released on the hg19 genome browser:

Chromatin Interactions by 5C from ENCODE/Univ. Mass(Dekker): This track contains chromatin interaction data generated using the 5C (Chromatin Conformation Capture Carbon Copy) method by the ENCODE group (Dekker Lab) at the University of Massachusetts. The track shows significant looping interactions between transcriptional start sites (TSS) and distal regulatory elements in the context of the 44 ENCODE pilot regions spanning 1% of the human genome.

ENCODE Pilot Regions: This track depicts the 44 target regions covering 1% of the human genome defined for the ENCODE pilot project. The hg19 coordinates for these regions were obtained using liftOver from the hg18 track.

Replication Timing by Repli-chip from ENCODE/FSU: This track shows genome-wide assessment of DNA replication timing in 7 cell types (3 stem cell, HeLa, IMR90, lymphoblastoid and BG02ES) using NimbleGen tiling CGH microarrays.

Gene Annotations from ENCODE/GENCODE Version 11: This version features 79% coverage of genes by manual annotation. It is based on the Ensembl 66 (Feb 2012) and Vega 46 (Jan 2012) gene predictions and curation.

Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB (Release 2): This release contains 68 new experiments, including 1 new cell line (HUVEC) and 20 new antibodies. There are also data corrections and new validation datasets (shRNA knockdown).

CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington (Release 3): This release contains 3 additional experiments in H7ES, NHLF, and HFF cell types.

DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington (Release 4): This release contains 11 new experiments across 9 new cell types.

Histone Modifications by ChIP-seq from ENCODE/Broad Institute (Release 2): This release contains 64 new experiments including 1 new cell line (Dnd41) and 10 new antibodies, and 3 datasets have additional data.

Open Chromatin by DNaseI HS from ENCODE/Duke (Release 2): This release provides data in additional cell lines (Colo29, CD4+, ECC-1, H7ES, HEK293T, 3 IPS lines derived from fibroblasts, MCF-7, Medullo, RWPE1, T-47D), higher-quality data for the K562 cell line, and additional data corrections and replacements.

Affymetrix Exon Array from ENCODE/Duke (Release 3): This track displays human tissue microarray data in 56 cell lines. The RNA extracted from these cells were also analyzed by DNaseI hypersensitivity (Duke DNaseI HS track), FAIRE (UNC FAIRE track) and ChIP-seq (UTA TFBS) by the ENCODE OpenChromatin group.

RNA-seq from ENCODE/Caltech (Release 3): Signal files for all experiments have been replaced with more accurate data. Earlier versions can still be accessed for download only.

29 Mar 2012 - Mouse ENCODE data releases: PSU TFBS, CSHL Long RNA-seq, LICR Histone (Rel 2), LICR TFBS (Rel 2)

Two new tracks and 2 track updates were released on the mm9 genome browser:

Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU: This track shows occupancy of genomic DNA by 5 transcription factors (CTCF, GATA1, GATA2, PAX5, TAL1) and Pol2 as determined by ChIP-seq in 6 erythroid and other blood cell types (CH12, MEL, G1E, megakaryocyte, erythroblast, G1E-ER4).

Long RNA-seq from ENCODE/Cold Spring Harbor Lab: This track contains information about mouse RNAs (> 200 nucleotides in length) in 17 different tissues, as obtained by Illumina squencing.

Histone Modifications by ChIP-seq from ENCODE/LICR (Release 2):
Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR (Release 2):

These two companion tracks survey cis-regulatory elements in the mouse genome. ChIP-seq was used to localize binding of Pol2, CTCF, and p300 factors and to profile 7 chromatin modification in 20 different mouse (C57Bl/6) tissues, primary cells, and cell lines. Release 2 of these tracks adds 87 new experiments.

24 Feb 2012 - Human ENCODE data releases: UW Repli-seq, HAIB RNA-seq, and 7 track updates

Two new tracks and 7 track updates were released on the hg19 genome browser:

Replication Timing by Repli-seq from ENCODE/University of Washington: This track shows genome-wide assessment of DNA replication timing in 15 cell lines as identified by the sequencing-based "Repli-seq" method. Replication timing is known to be an important feature for epigenetic control of gene expression that usually operates at a higher-order level than at the level of specific genes.

RNA-seq from ENCODE/HAIB: This track displays RNA-seq alignments and graphs of signal enrichment for 9 cell lines, in various treatment protocols. Estimates of transcript abundance are provided for download.

Gene Annotations from ENCODE/GENCODE Version 10: This version of the GENCODE Genes track features 77% coverage of genes by manual annotation. It corresponds to the Ensembl 65 (Dec 2011) and Vega 45 (Oct 2011) gene predictions and curation.

DNaseI Digital Genomic Footprinting from ENCODE/University of Washington (Release 3): Release 3 includes experiments in 19 additional cell types.

Histone Modifications by ChIP-seq from ENCODE/University of Washington (Release 3): This release adds the H7-hESC cell type and another replicate for the GM12865 experiment.

CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington (Release 2): Release 2 includes experiments in 15 additional cell lines.

DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA) (Release 2): Release 2 adds synthesis analysis for 10 cell types: Gliobla, GM12891, GM12892, GM18507, GM19239, HeLa-S3/IFNa4h, HTR8svn, Medullo, PanIslets, Urothelia

Small RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 2): This release adds 10 new cell lines (A549, AG04450, BJ, H1-hESC, HeLa-S3, HepG2, HUVEC, MCF-7, NHEK, and SK-N-SH_RA), a new displayed view (Contigs), and two new download files (GENCODE Predicted Exons and a Protocol Document).

RNA-seq from ENCODE/Caltech (Release 2): Data was reprocessed with a newer mapping algorithm (labeled V2). Additional download files of gene, transcript, and exon expression levels are now provided.

Genotype (CNV and SNP) by Illumina 1MDuo and CBS from ENCODE/HudsonAlpha (Release 2): This release contains data corrections to GM12878 and astrocyte experiments.

5 Jan 2012 - Human ENCODE data releases: UW Histone, HAIB Methyl450, RIKEN CAGE Loc, UW Affy Exon (Release 2)

Three new tracks and one track update were released on the hg19 genome browser:

Histone Modifications by ChIP-seq from ENCODE/University of Washington: This track shows genome-wide maps of histone modifications associated with active promoters (H3K4me3), repressed regions (H3K27me3), and active transcription (H3K36me3) in 57 cell types, as identified by ChIP-seq.

CpG Methylation by Methyl 450K Bead Arrays from ENCODE/HAIB: This track displays the methylation status of specific CpG dinucleotides in 61 cell types as identified by the Infinium Human Methylation 450 Bead Array platform. In general, methylation of CpG sites within a promoter causes silencing of the gene associated with that promoter.

RNA Subcellular CAGE Localization from ENCODE/RIKEN: This track from the ENCODE Transcriptome group shows 5' cap analysis gene expression (CAGE) tags and clusters. A total of 34 Experiments were conducted in 12 cell lines and one tissue (prostate), with RNA extracted from 6 isolated cellular compartments and in whole cell.

Affymetrix Exon Array from ENCODE/University of Washington (Release 2): This track from the ENCODE Transcriptome group shows human tissue miroarray data from the Affymetrix Human Exon 1.0 GeneChip. Release 2 of this track shows experiments in 14 additional cell lines.

1 Dec 2011 - Mouse ENCODE data releases: Caltech TFBS, Caltech Histone

Two new tracks were released on the mm9 genome browser:

Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech: This track shows 15 ChIP-seq experiments mapping 7 histone marks in the C2C12 myoblast cell line; both untreated cells and cells under timecourse treament with insulin to stimulate myogenesis.

Histone Modifications by ChIP-seq by ChIP-seq from ENCODE/Caltech: This track shows 26 ChIP-seq experiments mapping 14 transcription factors in the C2C12 myoblast cell line; both untreated cells and cells under timecourse treament with insulin to stimulate myogenesis.

10 Nov 2011 - ENCODE portal changes: New File Formats page and updates to Publications, Data Summaries, and Data Standards

The ENCODE portal was updated to include informative new and expanded pages. ENCODE-related data file formats are now documented on the new File Formats page. The Publications page was expanded to a comprehensive list of Consortium publications, plus methods, resource, and biological findings papers by ENCODE-funded projects. The Human Data Summary and Mouse Data Summary spreadsheets detailing ENCODE submissions were updated to reflect status as of the latest ENCODE quarterly reporting (Sept. 30 2011). Finally, the Data Standards section was greatly expanded to include new standards documents (v2.0 ChIP-seq) and a new Platform Characterization section.

29 Oct 2011 - Human ENCODE data releases: SYDH TFBS, CSHL Long RNA-seq, GIS RNA PET, UW DNaseI HS (release 3), Mappability (Release 3)

Three new tracks and two track updates were released on the hg19 genome browser:

Transcription Factor Binding Sites by ChIP-seq from Stanford/Yale/USC/Harvard: This comprehensive track shows 306 ChIP-seq experiments identifying transcription factor binding sites in 19 cell types.

Long RNA-seq from ENCODE/Cold Spring Harbor Lab: This comprehensive track from the ENCODE Transcriptome group shows RNAs longer than 200 nucleotides. Profiling was performed on RNA extracts enriched and depleted for polyA+, in multiple cellular compartments and whole cell, in 15 cell lines.

RNA Subcellular Localization by Paired End diTag Sequencing from GIS/ENCODE: This track from the ENCODE Transcriptome group shows starts and ends of full length mRNA transcripts determined by GIS paired-end ditag (PET) sequencing. Experiments were conducted in 7 cell lines and one tissue (prostate), with RNA extracted from 6 isolated cellular compartments and in whole cell.

19 Sept 2011 - Mouse ENCODE data releases: Stan/Yale Histone, LICR TFBS, LICR RNA-seq, Stan/Yale TFBS (Release 2)

Three new tracks and one track update were released on the mm9 genome browser:

Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale: This track shows locations of histone H3K4me3 modification in CH12 and MEL cell types. The two cell lines were selected for similarity to the ENCODE Tier1 cell lines (GM12878 and K562).

Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR, and RNA-seq from ENCODE/LICR: These tracks show transcriptome and Pol2, p300 and CTCF binding sites in mouse bone marrow, cerebellum, cortex, heart, kidney, liver, lung, spleen, embryonic fibroblast cells (MEFs) and embryonic stem (ES) cells.

Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale (Release 2): This release adds binding site localization for 13 additional transcription factors to the previously released TFBS track.

15 Sept 2011 - Summer ENCODE human data releases: GENCODE Genes V7, HAIB TFBS, Stanf Nucleosome, HAIB Genotype, SUNY RIP-seq, SUNY Switchgear

Six tracks of human ENCODE data were released in late summer on the hg19 genome browser:

Gene Annotations from ENCODE/GENCODE Version 7: The GENCODE Version 7 Genes track shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome. This version of GENCODE provides an increase of 25% in manual curation of transcripts over the previous (V4) version at UCSC.

Transcription Factor Binding Sites by ChIP-seq from ENCODE/HudsonAlpha: This track displays 185 experiments identifying transcription factor binding sites in multiple cell lines by chromatin immunoprecipitation followed by high throughput sequencing. A total of 56 transcription factor target antibodies and 20 cell types are represented.

Nucleosome Position by MNase-seq from ENCODE/Stanford/BYU: This track displays nucleosome position density maps from micrococcal nuclease digested chromatin in GM12878 and K562 cell lines. In the context of the ENCODE project, nucleosome positioning data are particularly valuable for analysis of the relationship between transcription factor binding, histone modifications, and gene activity.

Genotype (CNV and SNP) by Illumina 1MDuo and CBS from ENCODE/HudsonAlpha: This track displays copy number variation (CNV) as determined by the Illumina Human 1M-Duo Infinium HD BeadChip assay and circular binary segmentation (CBS). Allele frequency and single nucleotide polymorphism (SNP) data generated by the experiment are available for download.

RIP-seq from ENCODE/SUNY Albany: This track displays transcriptional fragments associated with RNA binding proteins in K562 and GM12878 cell lines, using Ribonomic profiling followed by high throughput sequencing.

RNA Binding Protein Associated RNA by SwitchGear from ENCODE/SUNY Albany: This track displays 3' UTR regions associated with RNA binding proteins in the HT-1080 cell line as evidenced by reporter assays.

8 July 2011 - Mouse ENCODE data releases: DNaseI hypersensitivity (UW DNaseI HS) and histone modifications (LICR Histone)

Two tracks of ENCODE data were released on the mm9 genome browser, from the UCSD/Ludwig Institute for Cancer Research and the University of Washington Mouse ENCODE groups.

Histone Modifications by ChIP-seq from ENCODE/LICR: This track shows a comprehensive survey of cis-regulatory elements in the mouse genome by using ChIP-seq to identify transcription factor binding sites and chromatin modification profiles in many mouse tissues and primary cells, including bone marrow, cerebellum, cortex, heart, kidney, liver, lung, spleen, mouse embryonic fibroblast cells (MEFs) and embryonic stem (ES) cells.

DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington: This track shows DNaseI sensitivity measured genome-wide in mouse tissues and cell lines using the Digital DNaseI methodology and DNaseI hypersensitive sites.

1 July 2011 - ENCODE data releases: Broad ChromHMM, Open Chrom Synth, UChicago TFBS, Duke Affy Exon

Four tracks of ENCODE production data and analysis were released in June, from the Broad Institute (Kellis lab), OpenChromatin (Duke, UNC, UT-A) and University of Chicago (White Lab) ENCODE groups. This is the first data release from the University of Chicago ENCODE group, which joined the Consortium as part of the NIH ARRA stimulus grants.

Chromatin State Segmentation by HMM from ENCODE/Broad: This track, and the companion hg18 track, display chromatin state segmentation of the human genome into fifteen states grouped to predict functional elements.

DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA): This track displays a synthesis of open chromatin regions and binding of selected regulatory factors, based on three complementary methodologies.

Affymetrix Exon Array from ENCODE/Duke: This track displays human tissue microarray data using Affymetrix Human Exon 1.0 ST expression arrays, including annotations at the gene level.

24 June 2011 - ENCODE RNA-seq data standards now available

The ENCODE Consortium has finalized 'Standards, Guidelines and Best Practices for RNA-Seq V1.0', as part of the Consortium's continuing effort to generate data standards. The document is available at the ENCODE portal via the Data Standards link.

RNA-Seq is a directed experimental approach aimed at characterizing transcription in biological samples. This document presents a set of guidelines and standards focused on best practices for creating 'reference quality' transcriptome measurements. sets.

1 June 2011 - ENCODE data releases in April and May

Five tracks of ENCODE production and analysis data were released in April and May on the GRCh37/hg19 human assembly from the Caltech, Broad Institute, HudsonAlpha Institute for Biotechnology, Duke University (Open Chromatin), SUNY Albany, University of Washington, Boston University, Stanford/Yale/Davis/Harvard and UCSC ENCODE groups

Integrated Regulation from ENCODE: This collection of tracks displays integrated signal and clustering annotations from multiple cell lines, using ENCODE primary data from RNA-seq, ChIP-seq, and DNase-seq assays. This track is a companion to the hg18 ENCODE Regulation track.

Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University): This track displays DNaseI hypersensitivity evidence as part of the four Open Chromatin track set.

RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany: This track displays transcriptional fragments associated with RNA binding proteins in different cell lines using RIP-Chip (Ribonomic) profiling on Affymetrix GeneChip� Human Gene 1.0 ST Arrays.

DNaseI Hypersensitivity by Digital DNaseI form ENCODE/University of Washington: This track shows DNaseI sensitivity measured genome-wide in different cell lines using the Digital DNaseI methodology.

OrChID Predicted DNA Cleavage Sites from ENCODE/Boston Univ (Tullius Lab): This track display predicted hydroxyl radical cleavage intensity on naked DNA for each nucleotide in the genome.

Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/Davis/Harvard: This track displays maps of histone modifications genome-wide using ChIP-seq in different cell lines.

22 April 2011 - ENCODE data releases: UTA TFBS, UW CTCF, UNC FAIRE, RIKEN CAGE Loc, UW Affy Exon, UW DNaseI DGF & Duke DNaseI HS

Seven tracks of ENCODE data on the GRCh37/hg19 human assembly were released in March and April from the University of Texas at Austin (Open Chromatin), University of Washington, University of North Carolina (Open Chromatin), RIKEN, and Duke University (Open Chromatin) ENCODE groups (6 of the tracks are new to hg19, and one is a Release 2 on hg19):

UTA TFBS: This track displays chromatin immunoprecipitation (ChIP-seq) evidence as part of the four Open Chromatin track sets.

UW CTCF: This track displays maps of genome-wide binding of the CTCF transcription factor in different cell lines using ChIP-seq high-throughput sequencing.

RIKEN CAGE Loc: This track shows 5' cap analysis gene expression (CAGE) tags and clusters in RNA extracts from different sub-cellular localizations in multiple cell lines.

UW Affy Exon: This track displays human tissue microarray data using Affymetrix Human Exon 1.0 GeneChip.

UW DNaseI DGF (Release 2): This track contains deep sequencing DNase data that will be used to identify sites where regulatory factors bind to the genome (footprints).

Duke DNaseI HS: This track displays DNaseI hypersensitivity (HS) evidence as part of the four Open Chromatin track sets.

14 February 2011 - ENCODE data releases: Caltech RNA-seq, Broad Histone, UW Histone & SUNY RIP Tiling

Four tracks of ENCODE data on the GRCh37/hg19 human assembly from the Caltech, Broad/MGH, SUNY Albany and University of Washington ENCODE groups were released:

Caltech RNA-seq: This track shows transcriptome measurements performed on polyA+ RNA using both stranded and unstranded protocols.

Broad Histone, UW Histone: These tracks display maps of histone modifications reflective of chromatin state changes identified by ChIP-seq.

SUNY RIP Tiling: This track displays transcriptional fragments associated with RNA binding proteins in different cell lines, using RIP-Chip (Ribonomic) profiling on Affymetrix GeneChip ENCODE 2.0R Tiling Arrays.

9 February 2011 - First Mouse ENCODE data release: Transcription Factor Binding Sites by ChIP-seq from Stanford/Yale

The first Mouse ENCODE data is now available on the mm9 (NCBI37) genome assembly. The Stan/Yale TFBS track in the 'Regulation' track group shows probable binding sites of the following transcription factors: c-MYB (H-141), CTCF (C-20), Max, NELFE, p300 (N-15), Rad21, and USF2, in the MEL leukemia (K562 analog) cell line as determined by ChIP-seq. Thanks to all who had a hand in generating this data and to the UCSC wrangler, Venkat Malladi, and Q/A staff who made this data release possible.

16 December 2010 - Release of DNA Methylation and DNaseI Sensitivity data

Three tracks of ENCODE DNA Methylation and DNaseI Sensitivity data have been released on the GRCh37/hg19 human assembly. All three tracks are in the browser 'Regulation' track group; one of the tracks is in the new ENC DNA Methyl super-track and the other two are in the new ENC DNase/FAIRE super-track (super-tracks provide additional documentation and organization by data type). The three newly released tracks are:

HAIB Methyl RRBS: This track reports the percentage of DNA molecules that exhibit cytosine methylation at specific CpG dinucleotides. In general, DNA methylation within a gene's promoter is associated with gene silencing, and DNA methylation within the exons and introns of a gene is associated with gene expression.

UW DNaseI DGF: This track contains deep sequencing DNase data that will be used to identify sites where regulatory factors bind to the genome (footprints).

UW DNaseI HS: This track shows DNaseI sensitivity measured genome-wide in different cell lines using the Digital DNaseI methodology and DNaseI hypersensitive sites.

Some of the data that comprise these tracks were originally released on hg18 and have been remapped to hg19; in such cases, subtracks have 'origAssembly hg18' as part of their metadata.

16 November 2010 - Release of the first ENCODE RNA-seq data on hg19

We are pleased to announce the release of the first ENCODE RNA-seq data on the GRCh37/hg19 human browser. Two tracks have just been released; these are organized in the new ENC RNA-seq super-track within the browser 'Expression' track group. The super-track provides additional documentation and organization by data type. The two tracks released are:

CSHL Sm RNA-seq: This track depicts NextGen sequencing information for RNAs between the sizes of 20-200 nt isolated from RNA samples from tissues or subcellular compartments from ENCODE cell lines.

GIS RNA-seq: This track shows high throughput sequencing of RNA samples from tissues or subcellular compartments from cell lines included in the ENCODE Transcriptome subproject.

All of the data that comprise these tracks were originally released on hg18 and have been remapped to hg19.

OpenHelix, together with the UCSC Genome Bioinformatics group, anounce a new online tutorial suite to teach users how to access the ENCODE data in the UCSC Genome Browser. This tutorial introduces the types of data available under ENCODE, and presents methods to access the data via the Genome Browser, Table Browser, and downloads. This tutorial suite is freely available at OpenHelix

We are pleased to announce the release of the first sets of production ENCODE data on hg19:

GIS DNA PET: This track shows the starts and ends of DNA fragments from different cell lines determined by paired-end ditag (PET) sequencing using different DNA fragment sizes for analysis of genome structural variation. The data in this track uses the new BAM data format. For more information about SAM/BAM, click here. All of the subtracks that comprise this track were originally released on hg18 and have been remapped to hg19.

Gencode Genes: This track (version 4, May 2010) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. Previous versions of this data were released on hg18, but this newest version is available solely on hg19.

We are pleased to announce the release of the ENCODE Integrated Regulation super-track, a collection of regulatory tracks containing state-of-the-art information about the mechanisms that turn genes on and off at the transcription level. Individual tracks within the set show enrichment of histone modifications suggestive of enhancer and promoter activity, DNAse clusters indicating open chromatin, regions of transcription factor binding, and transcription levels. When viewed in combination, the complementary nature of the data within these tracks has the potential to greatly facilitate our understanding of regulatory DNA.

The data comprising these tracks were generated from hundreds of experiments on multiple cell lines conducted by labs participating in the ENCODE project, and were submitted to the UCSC ENCODE Data Coordination Center for display on the Genome Browser.

Faced with the problem of how to display such a large amount of data in a manner facilitating analysis, UCSC has developed new visualization methods that cluster and overlay the data, and then display the resulting tracks on a single screen. Each of the cell lines in a track is associated with a particular color. Light, saturated colors are used to produce the best transparent overlay.

Currently, the ENCODE Regulation data are available only on the March 2006 (NCBI Build 36, UCSC version hg18) assembly of the human genome.

For a detailed description of the datasets contained in this super-track and a discussion of how the tracks can be used synergistically to examine regions of regulatory functionality within the genome, see the track description page.

"ENCODE whole-genome data in the UCSC Genome Browser": This paper addresses the history of the ENCODE project, summarizes the datasets available as of September 2009, and outlines methods to access the data. See Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5.

Initial release of the Caltech RNA-seq track: This track contains sequence reads and RPKM transcript abundance measures for sequences that map to either the genome or to known RNA splice sites. The results of four different mapping algorithms are provided, enabling comparison between different mapping algorithms.  Results are available for polyA+ and total RNA for the two ENCODE Tier 1 cell lines.

Release 2 of the Broad Histone track: This track displays maps of chromatin state generated using CHIP-seq.   Release 2 adds data for the ENCODE Tier 2 cell lines H1-hESC and HepG2, plus NHLF (normal human lung fibroblasts) and HMEC (human mammary epithelial) cells. This expands the track data to 9 cell lines, and 11 antibodies plus an input control.

Release 2 of the CSHL Long RNA-seq track: This track depicts sequencing of long RNAs of more than 200 nucleotides in length. Release 2 adds data from strand-specific assays of total RNA for the two ENCODE Tier 1 cell lines.

Release 2 of the ENCODE Open Chromatin track: This track displays evidence of open chromatin as identified by two complementary methods, DNaseI hypersensitivity and FAIRE, combined with ChIP identification methods. Release 2 adds data from eight additional cell types, expanding the track to 41 experiments in 13 cell lines.

Sep 2009 data freeze complete:  The ENCODE Consortium has just completed data submissions for the fourth production data freeze (Sep 09). The first set of data from this freeze to complete quality review is now available on the UCSC public server, in Release 2 of the ENCODE Transcription Factor Binding Sites from Yale/UC-Davis/Harvard track. Release 2 adds 59 ChIP-seq experiments to this track.

Other October track releases:  The Affymetrix/CSHL Subcellular RNA Localization by Tiling Array track was expanded to include 4 additional experiments.

encodeproject.org:  By request of the ENCODE Consortium, the domain encodeproject.org has been registered by the ENCODE Data Coordination Center, and is redirected to the ENCODE portal at UCSC.

New grants funded:  NHGRI has funded 5 new ENCODE grants, as part of the American Investment and Recovery Act. The new grants include expansion of ENCODE to the mouse genome and proteogenomics.

Job openings at UCSC:  The UCSC Genome Browser and ENCODE projects are currently accepting applications for Software Developer and Biological Database Testing/User Support Technician positions. We are looking for talented individuals who would like to use their skills in computer science, biology, and bioinformatics on fast-paced projects featuring the work of top genomics scientists worldwide.

During this period a total of 10 new ENCODE tracks were released to the UCSC public server. Functional elements and region characterization in these tracks include:

• DNaseI hypersensitive sites and hotspots (University of Washington)
• Regions of DNA methylation, by Methyl-seq and Illumina 27 array (HudsonAlpha Institute)
• Bi-directional promoters and negative regulatory elements (NHGRI Elnitski lab)
• Transcriptome profiling by RNA-seq, including single-molecule sequencing (CSHL, Helicos)
• Expression levels by exon array (University of Washington)
• Regions of copy number variation (HudsonAlpha Institute)
• Mappability/uniqueness of nmers (University of Massachusetts, Duke, Broad, Rosetta)

For track names and file access, see the Release Log and Downloads links listed in the left menu bar.

We would like to thank the contributing ENCODE labs and the the DCC team at UCSC for their efforts completing these tracks.

The following ENCODE tracks were released to the ENCODE DCC/UCSC public server during this period:

• Affymetrix/CSHL Subcellular RNA Localization by Tiling Array
• Open Chromatin, Duke/UNC/UT
• RIKEN RNA Subcellular Localization by CAGE Tags
• HudsonAlpha Transcription Factor Binding Sites by ChIP-seq
• Gencode Gene Annotations
• SUNY Albany RNA Binding Proteins by RIP-chip
• Histone Modifications by Broad Institute ChIP-seq

The Release Log listed in the left menu bar shows all released ENCODE tracks.

We would like to thank the HudsonAlpha, Transcriptome, Open Chromatin, Broad, and SUNY ENCODE groups and the DCC team at UCSC for their efforts completing these tracks.

We are pleased to announce the release to the ENCODE DCC/UCSC public server of the ENCODE Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard (Yale TFBS, in the Regulation group). This track shows probable binding sites of 12 transcription factors and RNA polymerase II in 7 cell types, as determined by chromatin immunoprecipitation followed by high-throughput sequencing. The Genome Browser displays discrete Peaks of enrichment and Signal graphs of enrichment density for these experiments. The sequence reads, quality scores, and sequence alignment coordinates from these experiments are available for download.

We would like to acknowledge the efforts of the Yale/UC-Davis/Harvard ENCODE group and the work of the UCSC data wrangler for this group, Tim Dreszer, for completing this track. We also thank the entire UCSC ENCODE team and the UCSC Quality Assurance group for contributing to this first ENCODE track release.

The February 2009 ENCODE data freeze supplements the data contributed for the November 2008 freeze, and will be used together with the earlier freeze for the initial analysis effort of the ENCODE Consortium. Data from this freeze is being incorporated into tracks created from the first data freeze, and is being reviewed by the UCSC Quality Assurance team.

The ENCODE Consortium has just completed the first freeze (November 2008) of whole-genome experimental data produced for the ENCODE production phase. Data submitted to the DCC for this freeze include:

• transcription factor binding sites
• histone modifications
• DNaseI hypersensitive sites
• DNA methylation
• transcription maps and tags, localized to subcellular compartments
• GENCODE gene annotations

Experiments during this freeze focused on the ENCODE Tier1 cell lines -- K562 leukemia, and GM12878 lymphoblastoid (which is also a 1000 Genomes project sample designated for in-depth analysis of genetic variation). The freeze also includes data from some ENCODE Tier2 and Tier3 cell lines (see Cell Types). The majority of these experiments were assayed by high-throughput sequencing (ChIP-seq, DNase-seq, and RNA-seq).

The UCSC quality team is currently reviewing these data. When the review is complete, the browser tracks and associated downloads will be released to the UCSC public Genome Browser.

Thanks to the many labs who contributed data for the initial phase of this project. We'd also like to acknowledge the UCSC ENCODE team for data wrangling during the freeze, and for the development and maintenance of the ENCODE automated data submission pipeline and associated tools: Kate Rosenbloom, Tim Dreszer, Larry Meyer, Michael Pheasant, Ting Wang, Galt Barber, and Andy Pohl.

The ENCODE browser for UCSC human genome assembly hg18 (NCBI Build 36) is now available. You can access the browser directly at http://genome.ucsc.edu/ENCODE/encode.hg18.html or by clicking the ENCODE link on the Genome Browser home page, then selecting the Regions (hg18) item in the sidebar menu on the ENCODE portal page.

The hg18 ENCODE browser includes 540 data tables in 59 browser tracks that were migrated from the hg17 browser. The hg17 data coordinates were converted to hg18 coordinates using the UCSC liftOver process.

To improve the accessibility of the data, related ENCODE tracks have been gathered into new configuration groupings ("super-tracks") that can be displayed or hidden using a single visiblity control. We have also reduced the number of track groups and have modified some of the group names for clarity.

The following table summarizes the data currently present in the hg18 ENCODE browser:

Group	Super-tracks	Tracks	Tables
Regions and Genes	2	12	73
Transcription	2	11	67
Chromatin Immunoprecipitation	8	28	349
Chromatin Structure	2	8	51

Note that the Variation and Comparative Genomics data were not lifted during this migration; instead, they will be replaced by new data. The first ENCODE MSA alignment for hg18 (TBA) is currently in progress on the UCSC development server.

During the migration, ENCODE tracks with whole-genome data were moved into the standard browser track groups. These include the GIS PET and UCSD/LI TAF1 tracks. Future submissions of whole-genome ENCODE data will be loaded directly into the standard track groups.

We have expanded the ENCODE downloads site to include original data for all "wiggle" datasets. These data files now have filename extensions indicating the wiggle input format (fixed step, variable step, or bedGraph).

You can find a description of the migration project and full details of the tables, tracks, and super-tracks available at the UCSC ENCODE portal on the UCSC genomeWiki.

The UCSC team members who contributed to this effort were: Andy Pohl (data conversion and database loading), Ting Wang and Donna Karolchik (super-track documentation), Bob Kuhn (portal updates), Brooke Rhead, Kayla Smith, and Ann Zweig (quality assurance), and Kate Rosenbloom (super-track development, project management).

The findings of the ENCODE project have been released to the public today, the culmination of a four-year effort to catalog the biologically functional elements in 1 percent of the human genome. The publications, which include a group paper in the 14 June 2007 issue of Nature and 28 companion papers in the June 2007 issue of Genome Research, were authored by researchers from academic, governmental, and industry organizations located in 11 countries. The Nature issue includes a pull-out poster featuring a screenshot of the UCSC Genome Browser displaying a broad range of the ENCODE data.

In the press release accompanying the publication rollout, NHGRI Director Francis S. Collins is quoted as saying "This impressive effort has uncovered many exciting surprises and blazed the way for future efforts to explore the functional landscape of the entire human genome. Because of the hard work and keen insights of the ENCODE consortium, the scientific community will need to rethink some long-held views about what genes are and what they do, as well as how the genome's functional elements have evolved. This could have significant implications for efforts to identify the DNA sequences involved in many human diseases."

For more information on the ENCODE project, including the consortium's data release and accessibility policies and a list of NHGRI-funded participants, see the NHGRI ENCODE website.

Between January and May of 2007, several new or upgraded data tracks were released by UCSC:

• Gencode March 2007 Genes and Gencode RACEfrags -- Reannotation of 69 loci consisting of 132 transcripts based on RACE, array, and sequencing analyses. New features include the addition of PolyA features, polymorphic gene type, and integration of experimental intron validation.
• Yale ChIP-chip RFBR -- Analysis of ChIP-chip data to identify regulatory factor binding regions, resulting from over 105 experiments representing 29 transcription factors in 9 cells lines, performed in 7 labs using 3 microarray platforms. Data provided by the ENCODE Transcriptional Regulation analysis group.
• University of Virginia DNA Replication Origins -- Three new datasets representing two new experimental methods for origin mapping (bubble trapping and nascent strand) in HeLa and GM06990 cells.
• University of Vienna RNAz -- RNA secondary structure prediction as predicted by RNAz, based on evolutionary conservation and thermodynamic stability.
• Duke DNaseI Hypersensitivity -- DNase-chip results in IMR90 (fibroblast), K562 (leukemia) and H9 (stem) cells.
• UCSC EvoFold -- Replaces TBA23 EvoFold.
• UC Davis ChIP Hits -- Updated cMyc and E2F1.

Thanks to the UCSC staff who worked on these tracks: Rachel Harte and Kate Rosenbloom (development), and Ann Zweig, Archana Thakkapallayil, and Kayla Smith (quality review).

To improve communication, we have posted instructions for our ENCODE ftp site on the ENCODE Wiki and have set up an email alias for notifying UCSC about your ENCODE data submissions: [email protected]. The current UCSC recipients are Kate Rosenbloom, Daryl Thomas, Ting Wang, and Rachel Harte.

During November and December, four new/improved data tracks were released:

• Chip-PET from the Genome Institute of Singapore - Genome-wide data for c-Myc in P493 B cells was added as a new subtrack (cMyc P493, encodeGisChipPetMycP493) to the existing GIS ChIP-PET track.
• DNaseI Hs from Duke University - Existing NHGRI data and new data from the Crawford lab at Duke University (raw and p-value data for the HepG2 cell line) were merged into the Duke/NHGRI DNase track. The newer data is based on DNase-chip technology.
• STAGE tags from University of Texas - Raw tags data for STAT1 in HeLa cells were added as a new subtrack (UT STAT1 HeLa Tags, encodeUtexStageStat1HelaTags) to the existing UT-Austin Stage track.
• DNaseI Hs from University of Washington - The existing three UW/Regulome DNaseI Sens tracks were replaced with a single new track (UW/Reg QCP DNaseI Sens) based on quantitative chromatin profiling (QCP) methods in 16 cell types.

Thanks to the UCSC staff who worked on these tracks: Rachel Harte, Kate Rosenbloom, and Hiram Clawson (development), Ann Zweig, Brooke Rhead, and Kayla Smith (quality review).

Twelve tracks of data produced by the ENCODE Multi-Species Sequence Analysis group have been released to the UCSC public server. These tracks contain multiple sequence alignments, conservation, and conserved (constrained) elements produced by four conservation methods (phastCons, binCons, GERP, SCONE) applied to three sequence alignments (TBA, MLAGAN, MAVID), and also an assessment of the agreement among the alignment methods. The alignments were based on genomic sequence in the ENCODE regions of 28 vertebrate species, as defined in the MSA September 2005 sequence freeze.

The following tracks can now be found in the ENCODE Comparative Genomics track group on the public ENCODE browser:

• MSA Consensus Constrained Elements
• TBA Alignments, TBA Conservation, TBA Conserved Elements
• MLAGAN Alignments, MLAGAN Conservation, MLAGAN Conserved Elements
• MAVID Alignments, Conservation, Conserved Elements
• MSA Alignment Agreement, MSA Alignment Gaps

Thanks to the following providers of this data:

• Elliott Margulies (NHGRI) - TBA alignments, binCons and phastCons conservation, Consensus elements, sequence freeze
• Daryl Thomas (Haussler lab, UCSC) - sequence freeze
• George Asimenos (Batzoglou lab, Stanford University) - MLAGAN alignments
• Colin Dewey (while at the Pachter lab, UC Berkeley) - MAVID alignments
• Greg Cooper (while at the Sidow lab, Stanford University) - GERP conservation
• Saurabh Asthana (Sunyaev lab, Harvard Genetics) - SCONE conservation
• Ariel Schwartz (Pachter lab, UC Berkeley) - Alignment agreement

Also, thanks to the UCSC team that produced these tracks in the browser: Kate Rosenbloom (track development), Ann Zweig, Kayla Smith, and Archana Thakkapallayil (quality review).

Since mid-June, UCSC has released new ENCODE data from three labs (Sanger Institute, Uppsala University, and University of North Carolina) and has a track in progress for newly submitted data from a fourth lab (NHGRI/Duke University):

• Sanger ChIP-chip (MOLT4 and PTR8 cells) - Eight new datasets were added to the Sanger Chip/chip track. The new data show sites of H3 histone methylation and acetylation in MOLT4 (lymphoblastic leukemia) and also in the chimpanzee PTR8 cell line, used for comparative analysis. Thanks to Rob Andrews at the Ian Dunham lab for providing these data.
• Uppsala University Chip/chip Butyrate - This track shows the effects of Na-butyrate treatment of HepG2 (liver carcinoma) cells on histone H3 and H4 acetylation, assayed on Sanger microarrays. Thanks to Adam Ameur at the Claes Wadelius lab for providing these data.
• University of North Carolina FAIRE (Peaks data update) - This track was updated to include a subtrack of peaks generated by an alternate peak-finding algorithm, ChIPOTle. The FAIRE data were generated from 2091 fibroblast cells hybridized to NimbleGen ENCODE arrays. Thanks to Paul Giresi at the Jason Leib lab for providing these data.
• NHGRI DNaseI-HS Raw (in progress) - DNase-chip raw and p-value data in GM06990, CD4+, and Hela S3 cells.

Thanks to our UCSC staff who worked on these tracks: Rachel Harte and Hiram Clawson (development), Ann Zweig and Archana Thakkapallayil (quality review), and Donna Karolchik (documentation).

The ENCODE data status page has been updated to reflect the recent activity.

During the build-up to the analysis paper submissions, UCSC received a flurry of ENCODE data submissions (6 during the month of May). We have recently released three data sets to our public server; the remaining tracks are in progress, as indicated below.

Released data:

• Sanger ChIP-chip (HFL-1 cells) - New data added to the Sanger ChIP track show the location of modified histones in HFL-1 (embryonic lung fibroblast) cells. Thanks to Rob Andrews and Christopher Koch for providing this data.
• DLESS (Detection of LinEage Specific Selection) - This track shows elements predicted by the DLESS program to be under lineage-specific selection, based on alignments of 17 mammalian species from NHGRI/PSU TBA ENCODE alignments. DLESS is based on a phylo-HMM with states for neutrally evolving and conserved regions, and for gains and losses on each branch of the tree. Thanks to Adam Siepel of Cornell University, who developed the DLESS program, generated the data, and loaded the annotation track.
• UW/Regulome Dnase/Array - This track displays DNaseI sensitivity in GM06990 cells, using the DNase/Array methodology. Dnase/Array is a novel method for isolating DNA segments corresponding to specific DNaseI cleavage events on individual nuclear chromatin templates. Thanks to Scott Kuehn at the University of Washington for providing these data.

Thanks to our UCSC staff who worked on these tracks: Rachel Harte (development), Ann Zweig, Kayla Smith, and Archana Thakkapallayil (quality review).

In quality review:

• UNC FAIRE Peaks (Update, 2091 fibroblasts)

In progress:

• University of Uppsala Chip/Chip (butyrate treatment in HepG2)
• UW/Regulome QCP Dnase HS (update and new cell lines -- 16 tissues)
• PECAN Alignments from EBI

The ENCODE data status page has been updated to reflect the recent activity.

All datasets submitted for the October 2005 ENCODE freeze have now been released. The tracks with their release dates are:

• 13 Jan. - Yale ChIP-chip (5 new transcription factors)
• 3 Jan. - University of Uppsala Chip/chip (data correction)
• 2 Jan. - Yale RNA (update)
• 29 Dec. - U Virginia DNA Replication Timing and Predicted Origins
• 28 Dec. - UT Austin STAGE
• 21 Dec. - Affy RNA and Transfrags (HeLa update)
• 22 Nov. - Sanger ChIP-chip (5 histone modifications)
• 19 Nov. - UC Davis ChIP-chip (Pol2, Myc) in HeLa
• 18 Nov. - U North Carolina FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)
• 1 Nov. - Affy RNA and Transfrags (update)
• 1 Nov. - UT-Austin Ng ChIP-chip (E2F4, c-Myc factors)
• 1 Nov. - GIS PET RNA (update)
• 1 Nov. - Gencode Genes and Introns (update)
• 1 Nov. - NHGRI DNaseI HS (update and new GM06990)
• 27 Oct. - UCSD/LI Ng ChIP-chip (update and new TFs)
• 14 Oct. - GIS ChIP/PET (STAT1)
• 21 Sep. - Boston University ORChID (update)

The ENCODE browser for UCSC human genome assembly hg17 (NCBI Build 35) is now available at http://genome.ucsc.edu/ENCODE/encode.hg17.html and from the Regions (hg17) item in the left (blue bar) menu of the ENCODE portal.

All datasets originally submitted in hg17 coordinates for the June data freeze were directly loaded; the remaining data were coordinate-converted using the UCSC liftOver process. A total of 351 data tables were loaded into our database. NOTE: Many of these tracks will be updated with new data from the October ENCODE data freeze.

Many thanks to all the ENCODE consortium members who contributed data for this release. We'd also like to thank UCSC team members Kate Rosenbloom for portal and track development and Jennifer Jackson, Kayla Smith, Ann Zweig, and Bob Kuhn for quality assurance.

The remaining datasets submitted for the June 2005 ENCODE data freeze have now been released as annotation tracks in the hg16 browser. These tracks and their release dates are:

• 15 Jul. - TBA23 EvoFold RNA Structure Predictions
• 14 Jul. - Regulome DNaseI HS and Sens
• 14 Jul. - Regulome Plate Q/A and Amplicons
• 14 Jul. - MSA Consensus Elements
• 14 Jul. - TBA alignments with Conservation
• 14 Jul. - Stanford MLAGAN Alignments and Conservation
• 13 Jul. - Oxford Recombination

Several new ENCODE data sets have been released in the UCSC Genome Browser.

EGASP Full, Partial, and Update: These three gene prediction tracks are from the ENCODE Gene Annotation Assessment Project (EGASP) Prediction Workshop 2005. The EGASP Full track shows 20 sets of gene predictions originally submitted for the workshop, covering all 44 ENCODE regions. THE EGASP Partial track shows eight sets of gene precdictions that were submitted for the workshop, but do not cover all ENCODE regions. The EGASP Update track shows updated versions of some of the submitted predictions. Thanks to Julien Lagarde at IMIM for providing the EGASP Full and EGASP Partial data sets. Thanks to Tyler Alioto of IMIM (GeneID-U12 and SGP2-U12), Deyou Zheng of Yale (Yale Pseudogenes), Sarah Djebali of Ecole Normale Sup�rieure (Exogean), Jonathan Allen of TIGR/Univ. Maryland (Jigsaw) and Mario Stanke of the University of Gottingen (Augustus) for providing their EGASP Update gene sets.

RIKEN CAGE Predicted Gene Start Sites: This track shows the numbers of 5' cap analysis gene expression (CAGE) tags that map to the genome at specific locations. Areas in which many tags map to the same region may indicate a significant transcription start site. Thanks to Albin Sandelin at RIKEN and the FANTOM (Functional Annotation of Mouse) Consortium for providing these data.

Stanford RTPCR: This track displays absolute transcript copy numbers for 136 genes and 12 negative control intergenic regions, determined by real-time PCR in HCT116 cells.

Stanford ChIP-chip, Stanford ChIP-chip Smoothed Score: These tracks display raw scores and sliding-window mean scores for regions bound by the Sp1 and Sp3 transcription factors in three cell lines (HCT116, Jurkat, K562), assayed by chromatin immunoprecipitation and hybridization to Nimblegen oligo tiling arrays. The Smoothed Score track is provided solely for visualization purposes -- the raw scores should be used for data analysis.

Stanford Methylation Digest: This track displays experimentally determined regions of unmethylated CpGs in eight cell lines (BE2C, CRL1690, HCT116, HT1080, HepG2, JEG3, SNU182, and U87MG). Genomic DNA was digested with a cocktail of six methyl-sensitive restriction enzymes, size-selected, amplified, labeled, and hybridized to Nimblegen oligo tiling arrays.

Thanks to Nathan Trinklein for providing the Stanford datasets.

We'd like to acknowledge the work of the UCSC Genome Bioinformatics team members who produced these tracks: Kate Rosenbloom, Angie Hinrichs, and Hiram Clawson (development), Ann Zweig, Bob Kuhn, Galt Barber, Rachel Hart, and Ali Sultan-Quarrie (quality review), and Donna Karolchik (documentation).

The first datasets in the ENCODE Variation group are now available in the UCSC browser.

NHGRI Deletion/Insertion Polymorphisms: All human trace data from NCBI's trace archive were aligned to the genome and processed using the programs ssahaSNP and ssahaDIP to detect deletion and insertion polymorphisms. Thanks to Jim Mullikin at NHGRI for performing the analyses and providing these data.

HapMap Allele Frequencies: This track shows allele frequencies for the four HapMap populations in the ten ENCODE regions that have been resequenced for variation (manually selected regions m010, m013, and m014 and randomly selected regions r112, r113, r123, r131, r213, r232, and r321). These data were obtained from HapMap public release #16c.1. Thanks to the International HapMap Project for making this information available.

Sanger Genotype-Expression Association: This track displays associations among gene expression data from the 60 unrelated Centre d'Etude du Polymorphisme Humain (CEPH) individuals of the International HapMap Project with SNPs genotyped by HapMap, in eight ENCODE regions (m010, m013, m014 and r123, r131, r213, r232, and r321). The CEPH population is composed of Utah residents with ancestry from northern and western Europe. The expression data were generated with the Illumina platform at the Wellcome Trust Sanger Institute. Thanks to Manolis Dermitzakis at the Sanger Institute for providing these data.

We'd also like to acknowledge the UCSC ENCODE team members who worked on these tracks: Heather Trumbower, Daryl Thomas, and Angie Hinrichs (development), Galt Barber and Ali Sultan-Qurraie (quality assurance), and Donna Karolchik (documentation).

To aid ENCODE analysis and reduce visual clutter, we have split the Genome Browser ENCODE track group into six new groups:

• ENCODE Regions and Genes
• ENCODE Transcript Levels
• ENCODE Chromatin Immunoprecipitation
• ENCODE Chromosome, Chromatin and DNA Structure
• ENCODE Variation
• ENCODE Comparative Genomics

We have also released a set of new Yale data and an extensive update of Affymetrix data. The track controls for these datasets can be found in the track groups ENCODE Transcript Levels and ENCODE Chromatin Immunoprecipitation.

Yale ChIP-chip and RNA: Three tracks of ChIP-chip data from Yale, evaluating microarray platforms, have been released: Yale ChIP pVal, Yale ChIP Sig, and Yale ChIP Sites. These tracks show results of ChIP experiments using STAT1 antibody in HeLa cells on four different microarrays -- three custom maskless photolithographic oligo arrays, designed at different resolutions, and the PCR amplicon array developed by the Ren lab at the Ludwig Institute/UCSD.

Two tracks of RNA transcript data from Yale have been released: Yale RNA and Yale TAR. These tracks show transcriptionally active regions and transcribed fragments for three cell types (neutrophil, placenta, and NB4 variously treated for differentiation).

Thanks to Joel Rozowsky at Yale for providing this data. Additional Yale ChIP-chip data is currently under review by our quality assurance group.

Affymetrix ChIP-chip and RNA: The Affymetrix ChIP-chip dataset now contains experimental results for ten factors (Brg1, CEBPe, CTCF, H3K27me3, H4Kac4, P300, PU1, Pol2, RARA, and SIRT1) in HeLa cells at four timepoints after retinoic acid treatment, plus TFIIB for the final timepoint only. The data is displayed in eight tracks: Affy PVal 0h, 2h, 8h, 32h and Affy Sites 0h, 2h, 8h, 32h. We acknowledge that this track grouping is a bit awkward and are working composite track enhancements to provide more flexibility.

The Affy RNA tracks show RNA abundance and transfrags in retinoic acid-stimulated HL-60 cells at four timepoints, and in GM06990 and HeLa cells: Affy RNA Signal and Affy Transfrags.

Thanks to Stefan Bekiranov and Srinka Ghosh at Affymetrix for providing these data.

Thanks also to the UCSC ENCODE team members who developed and reviewed these tracks and to Rachel Harte in the UCSC browser group for her assistance with track review.

Six more ENCODE annotation tracks have been added to the Genome Browser this week:

NHGRI DNaseI-Hypersensitive Sites (update): The NHGRI DNaseI-HS track has been updated with new data. The track now includes DNaseI-hypersensitive sites in CD4+ T-cells before and after activation by anti-CD3 and anti-CD28 antibodies. Thanks to Greg Crawford at the Collins lab (NHGRI) for providing these data.

Genome Institute of Singapore PET of PolyA+ RNA: The GIS PET RNA track displays starts and ends of mRNA transcripts determined by paired-end ditag sequencing in two cell lines, MCF7 and HCT116 treated with 5 fluoro-uracil. A total of 584,624 PETs were generated for MCF7 and 280,340 were generated for HCT116. More than 80% of the PETs in each group were mapped to the genome. Thanks to Atif Shahab, Yijun Ruan, the GIS, and the Bioinformatics Institute of Singapore for providing these data.

Gencode Gene Annotations and Intron Validation: The Gencode Genes track displays high-quality manual annotations in the ENCODE regions generated by the GENCODE project. A companion track, Gencode Introns, shows experimental gene structure validations for these annotations. Thanks to the HAVANA team at the Wellcome Trust Sanger Institute; France Denoeud, Julien Lagarde, and Roderic Guigo at the IMIM; and Alexandre Reymond at the University of Geneva for providing the annotations and experimental confirmation, as well as working with UCSC to develop the track display.

Boston University Hydroxyl Radical Cleavage: The BU ORChID track displays predicted hydroxyl radical cleavage intensity on naked DNA for each nucleotide in the ENCODE regions. The prediction algorithm draws data from a database of 150 experimentally-determined cleavage patterns. Thanks to Jay Greenbaum at the Tullius lab for providing these data.

UC Davis ChIP-chip: The UCD Ng E2F1 track shows ChIP analysis of HeLa cells using E2F1 antibody as assayed on Nimblegen arrays. The E2F1 factor is associated with cell cycle control, transcriptional regulation, and apoptosis. Thanks to the Farnham lab and Kyle Munn, Todd Richmond and Roland Green of Nimblegen for providing these data.

Ludwig Institute/UCSD ChIP-chip: Three tracks of ChIP-chip data using Nimblegen arrays have been released: LI Ng TAF1 IMR90, LI Ng Validation, and LI Ng gIF ChIP. The TAF1 track shows genome-wide TAF1 binding sites as determined by ChIP in IMR90 (fibroblast) cells assayed on Nimblegen high-density oligo arrays. The peaks from the genome scan experiments were verified using four antibodies associated with transcription start (Pol2, H3ac, H3K4me2, and TAF1) on condensed arrays covering the putative TAF1 binding sites. The gIF track shows the results of ChIP-chip experiments using gamma interferon-treated HeLa cells, with Pol2 and H3K4me3 antibodies.

Two additional tracks, LI ChIP Various and LI gIF ChIP, display ChIP-chip data assayed on Ren lab ENCODE PCR tiling arrays for five antibodies (Pol2, TAF1, H3K4me2, SUZ12, H3K27me3) and four cell lines (HeLa, THP1, IMR90, HCT116), as well as gamma interferon experiments using seven antibodies (Pol2, TAF1, H3K4me2, H3K4me3, H3ac, H4ac, and STAT1) in HeLa cells. Thanks to Chunxu Qu and Bing Ren, at the Ren lab for providing these data and assisting with track display issues.

We'd also like to acknowledge the UCSC team members who developed these tracks: Kate Rosenbloom, Hiram Clawson, and Angie Hinrichs for track development; Bob Kuhn, Ali Sultan-Qurraie and Galt Barber for quality assurance; and Donna Karolchik and Jim Kent for documentation.

The Sanger Institute has submitted ChIP-chip data for additional antibodies and cell lines, which we have incorporated into the existing Sanger ChIP browser track. The expanded track now contains data for five antibodies (H3K4me1, H3K4me2, H3K4me3, H3ac, H4ac) and two cell lines (GM06990, K562 (leukemia)).

Thanks to Rob Andrews and Chris Koch at the Dunham lab for providing these data. UCSC team members who developed this track include Hiram Clawson (track development), Ali Sultan-Qurraie (quality assurance), and Donna Karolchik and Jim Kent (documentation).

We have modified the Genome Browser labels for the existing ENCODE data tracks to trim overly-long labels that were truncated in the display and to facilitate cross-track analysis. The new label format shows the submitter and the experiment, followed by the cell line (in tracks where the data includes only one cell line).

We are pleased to announce the first UCSC Genome Browser tracks released for the June 2005 ENCODE data freeze: Stanford Promoters and UVa DNA Replication Temporal Profiling.

Stanford has provided an update of their promoter activity data based on transient transfection luciferase reporter assays of 643 putative promoter fragments in the ENCODE regions. The update includes two additional cell lines and activity averaged across all cell lines. The data tables now contain additional experimental detail to facilitate analysis. This track, containing 17 subtracks (16 cell lines and the average), is labeled "Stanf. Promoter". Thanks to Sara Hartman at the Myers lab for providing these data.

The Dutta lab at Univerity of Virginia (UVa) has completed the second biological replicate of their temporal profiling of HeLa cell replication products and has provided a dataset containing merged data from the two replicates. The track, containing five subtracks representing two-hour intervals, is labeled "UVa DNA Rep". Thanks to Christopher Taylor at the Dutta lab for providing these data.

We'd also like to acknowledge the UCSC team members who worked on these annotation tracks: Angie Hinrichs (track development), Galt Barber and Ali Sultan-Qurraie (QA), and Jim Kent and Donna Karolchik (track documentation).

A new ENCODE MSA sequence data freeze is available on the UCSC downloads server. The latest freeze contains sequences from 23 vertebrates provided by NISC, Baylor, the Broad Institute (2X) and the whole genome shotgun (WGS) assemblies. The data may be downloaded as individual data files or a directory tarball. Aligners are encouraged to upload alignments and related data (such as conservation scores and elements) to the UCSC ENCODE ftp site as soon as possible and then notify Kate Rosenbloom. Other data, (conservation, trees, etc.) will be generated based on this dataset.

The following is a summary of data updates from the previous release:

• The human assembly version remains at hg16 (Jul. 2003).
• The mouse assembly has been updated from mm5 (May 2004) to mm6 (Mar. 2005).
• The multiple rat sequences have been replaced by a single sequence: rn3 (Jun. 2003).
• The cow sequences have been updated using an assembly of BAC-based sequences provided by Baylor College of Medicine.
• Fugu (fr1), macaque (rheMac1), opossum (monDom1), Tetraodon (tetNig1), Xenopus (xenTro1), and zebrafish (danRer2) have been added. The macaque sequence was obtained from a Baylor College of Medicine assembly that has not yet been officially released.
• A new NISC species, rfbat (Rhinolophus ferrumequinum), is now available.
• Platypus data from regions where NISC has not yet generated data were provided by Jim Mullikin from a preliminary assembly of Washington University WGS reads.
• This freeze includes low-redundancy sequence data from tenrec, elephant, armadillo, and rabbit. Only one set of sequences are provided per species/target combination; where available, NISC data is provided instead of the 2X assemblies. These data are not yet accessioned at NCBI, but were made available by the Broad Institute (rabbit, elephant, armadillo) and Jim Mullikin (tenrec).
• Orthology predictions for Fugu were made only by MAVID/Mercator; predictions for all other assemblies supported by the UCSC Genome Browser represent a union with UCSC predictions as well. Because no additional post-processing was done on the Fugu predictions, they contain a few very small contigs.

Thanks to the many people, particularly Elliott Margulies and Daryl Thomas, who made this release possible.

The ENCODE Genome Browser now features the ChIP-PET/GIS annotation track, which shows paired-end ditag (PET) sequences derived from 65,572 individual p53 ChIP fragments of 5-fluorouracil (5FU) stimulated HCT116 (colon) cells. Only PETs with a single specific mapping to the genome are included in this track.

Thanks to Atif Shahab, Chia-Lin Wei, and Yijun Ruan at the Genome Institute of Singapore for providing the p53 ChIP-PET library and sequence data. The data were mapped and analyzed by scientists from the Genome Institute of Singapore, the Bioinformatics Institute, Singapore, and Boston University. For more information about this annotation, see the ChIP-PET/GIS track description page.

The First Exon/BU annotation track, contributed by the ZLAB at Boston University, is now available in the UCSC Genome Browser. This track displays expression levels of computationally identified first exons and a constitutive exon of 20 genes in the ENCODE regions.

For each gene, all alternative first exons were identified based on manual selection of predictions from the PromoSer program. The expression levels of exons were then quantified using rcPCR in ten normal human tissues.

Thanks to Ulas Karaoz and the Zhiping Weng lab at Boston University for providing these data. For more information about this annotation, as well as a complete list of the individuals who contributed to this track, see the First Exon/BU track description page.

A simple summary page has been added to the UCSC ENCODE portal to show the status of datasets submitted to UCSC by ENCODE contributors. The page may be found at http://genome.ucsc.edu/ENCODE/trackStatus.html and can be accessed via links on the ENCODE home page and the ENCODE data submission page. The status page will be updated approximately once a week.

To review the latest ENCODE data releases, see the release log.

Two additional sets of ChIp/Chip data from UCSD/Ludwig Institute are now available:

    ChIp/LI AcH3     
    ChIp/LI MeH3K4   

To consolidate viewing in the browser, the previously released eight datasets from UCSD/LI have been reformatted as two composite tracks (one track per antibody) with each track containing four subtracks (one per cell line). These tracks are:

    ChIp/LI Pol2
    ChIp/LI TAF1

Thanks to Chunxu Qu and the Ren lab for providing these data.

The ENCODE download area has been reorganized and updated on our public download server. The downloads access page is now:

        http://hgdownload.cse.ucsc.edu/goldenPath/encode/

and the annotations are now located in the assembly-specific download directory, currently:

        http://hgdownload.cse.ucsc.edu/goldenPath/hg16/encode/

Any web pages referencing the previous UCSC ENCODE downloads will need to be updated. Please contact us if you have any difficulties.

A second set of ENCODE ChIp/Chip data is now available on the July 2003 human genome assembly:

    ChIp/Affy Pol2 Pval
    ChIp/Affy Pol2 Sites
    RNA/Affy Signal
    RNA/Affy Sites

A new composite track display was developed to concisely display multiple data sets of similar types, a common feature of ENCODE data. Each of these new tracks contains 4 subtracks, one for each time interval. The subtracks share a single description page and set of visibility controls. Checkboxes on the track configuration page allow selected subtracks to be hidden in the display.

These data were generated and analyzed by Tom Gingeras' group at Affymetrix and Kevin Struhl's group at Harvard Medical School. We would like to thank Stefan Bekiranov at Affymetrix for submitting the data and working closely with us to clarify the experimental methods and verification descriptions.

The first datasets submitted for the ENCODE project are now publicly available:

• ChIP-chip and transcription (Ludwig Institute/UCSD)
• Temporal profiling of DNA replication (University of Virginia)
• Promoter activity (Stanford)
• DNaseI hypersensitive sites (NHGRI)

We are pleased to release the first "official" sequence data freeze for the ENCODE multiple sequence alignment projects. The data formats are described in the README file, and the sequences and supporting information is collected in the data directory.

The species included in this freeze are as follows:

       _SPECIES_      _SOURCE_
        Human           hg16
        Chimpanzee      panTro1
        Dog             canFam1
        Rat             rn3
        RatB	        BCM
        Mouse           mm5
        Chicken		galGal2
        Galago		NISC
        Baboon		NISC
        Marmoset        NISC
        Armadillo       NISC
        Platypus        NISC

Please note that we have also included a *second* rat sequence (ratB) in this freeze. RatB represents an initiative to standardize the quality level of sequences in the ENCODE regions for species with genome-wide sequence data. The data were made available just before our freeze date, so we decided to include both versions of the rat sequence for now. Eventually these sequences will likely be rolled into future genome assemblies.

Remember, this is a work in progress, so not all targets have sequence from all species. And some species/target combinations may not be complete yet. Progress on the NISC-generated sequences can be found at the NISC ENCODE Project: Comparative Sequencing.

Many people have worked very hard to make these data available. Special thanks to Daryl Thomas, Kate Rosenbloom and the entire UCSC Team; Greg Schuler and the NCBI team; Colin Dewey and Lior Pachter; Pam Thomas and the NISC team; and David Wheeler and the BCM team.

Please send any comments to the ENCODE MSA Mailing List.

    Elliott
--
Elliott H. Margulies, Ph.D. Genome Technology Branch, NHGRI

We are proud to announce the release of features in the UCSC Genome Browser that are tailored to the ENCODE project community, including this home page to consolidate these resources.

The initial resources include sequences for the current human assemblies (hg16, hg15, hg13, and hg12), sequence of the comparative species from NISC, tools for coordinate conversion between human assemblies, format descriptions for data submission, and contact information for help with submitting annotation data and analyses.

Bulk downloads of the sequence and annotations may be obtained from the ENCODE Project Downloads page. The sequences available here are repeat-masked versions of the GenBank records.